Abstract BackgroundLoaches from the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth, and some species of loach inhabit the underground drainage. The genus Oreonectes with 18 currently recognized loach species represent the three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable research resource of the evolution of cavefishes.ResultWe assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. The genome assembly contains 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. Meanwhile,we found that dozens of genes related to eye development and melanogenesis were pseudogenised during the evolutionary process in cave environment, providing novel insights into complex phenotypic adaptations of animals in specific environment. ConclusionHere we report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. This genome assembly will contribute to the study of the evolution and adaptation of cavefishes within Oreonectes and beyond (Cobitidea) and provid valuable genomic resources for studies on the evolutionary history of the rapid speciation processes of family Nemacheilidae.